extracting substrings from a file

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  • sofiafig@gmail.com
    #1

    extracting substrings from a file

    Hi,

    I have a file with several entries in the form:

    AFFX-BioB-5_at E. coli /GEN=bioB /gb:J04423.1 NOTE=SIF
    corresponding to nucleotides 2032-2305 of /gb:J04423.1 DEF=E.coli
    7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB),
    7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and
    dethiobiotin synthetase (bioD), complete cds.

    1415785_a_at /gb:NM_009840.1 /DB_XREF=gi:6753 327 /GEN=Cct8 /FEA=FLmRNA
    /CNT=482 /TID=Mm.17989.1 /TIER=FL+Stack /STK=281 /UG=Mm.17989 /LL=12469
    /DEF=Mus musculus chaperonin subunit 8 (theta) (Cct8), mRNA.
    /PROD=chaperonin subunit 8 (theta) /FL=/gb:NM_009840.1 /gb:BC009007.1

    and I would like to create a file that has only the following:

    AFFX-BioB-5_at /GEN=bioB /gb:J04423.1

    1415785_a_at /gb:NM_009840.1 /GEN=Cct8

    Could anyone please tell me how can I do it?

    Many thanks in advance
    Sofia

    Tags: None
    • Tim Chase
      #2
      Re: extracting substrings from a file

      I have a file with several entries in the form:
      >
      AFFX-BioB-5_at E. coli /GEN=bioB /gb:J04423.1 NOTE=SIF
      corresponding to nucleotides 2032-2305 of /gb:J04423.1 DEF=E.coli
      7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB),
      7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and
      dethiobiotin synthetase (bioD), complete cds.
      >
      1415785_a_at /gb:NM_009840.1 /DB_XREF=gi:6753 327 /GEN=Cct8 /FEA=FLmRNA
      /CNT=482 /TID=Mm.17989.1 /TIER=FL+Stack /STK=281 /UG=Mm.17989 /LL=12469
      /DEF=Mus musculus chaperonin subunit 8 (theta) (Cct8), mRNA.
      /PROD=chaperonin subunit 8 (theta) /FL=/gb:NM_009840.1 /gb:BC009007.1
      >
      and I would like to create a file that has only the following:
      >
      AFFX-BioB-5_at /GEN=bioB /gb:J04423.1
      >
      1415785_a_at /gb:NM_009840.1 /GEN=Cct8
      >
      Could anyone please tell me how can I do it?
      The following seems to do it for me...

      outfile = file('out.txt', 'w')
      for line in file('in.txt'):
      if '/GEN' in line and '/gb:' in line:
      newline = []
      for index, item in enumerate(line. split()):
      if index == 0 or item.startswith ('/GEN')
      or item.startswith ('/gb:'):
      newline.append( item)
      outfile.write(' \t'.join(newlin e))
      outfile.write(' \n')
      outfile.close()


      There are some underdefined conditions...I presume that both the
      GEN and gb: have to appear in the line. If only one of them is
      required, change the "and" to an "or".

      -tkc



        Comment

        • John Machin
          #3
          Re: extracting substrings from a file

          sofiafig@gmail. com wrote:
          Hi,
          >
          I have a file with several entries in the form:
          >
          AFFX-BioB-5_at E. coli /GEN=bioB /gb:J04423.1 NOTE=SIF
          corresponding to nucleotides 2032-2305 of /gb:J04423.1 DEF=E.coli
          7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB),
          7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and
          dethiobiotin synthetase (bioD), complete cds.
          >
          1415785_a_at /gb:NM_009840.1 /DB_XREF=gi:6753 327 /GEN=Cct8 /FEA=FLmRNA
          /CNT=482 /TID=Mm.17989.1 /TIER=FL+Stack /STK=281 /UG=Mm.17989 /LL=12469
          /DEF=Mus musculus chaperonin subunit 8 (theta) (Cct8), mRNA.
          /PROD=chaperonin subunit 8 (theta) /FL=/gb:NM_009840.1 /gb:BC009007.1
          >
          and I would like to create a file that has only the following:
          >
          AFFX-BioB-5_at /GEN=bioB /gb:J04423.1
          >
          1415785_a_at /gb:NM_009840.1 /GEN=Cct8
          >
          Could anyone please tell me how can I do it?
          >
          Many thanks in advance
          Sofia
          Here's my first iteration:
          C:\junk>type sofia.py
          prefixes = ['/GEN=', '/gb:']

          def extract(fname):
          f = open(fname, 'r')
          chunks = [[]]
          for line in f:
          words = line.split()
          if words:
          chunks[-1].extend(words)
          else:
          chunks.append([])
          for chunk in chunks:
          if not chunk:
          continue
          output = [chunk[0]]
          for word in chunk:
          for prefix in prefixes:
          if word.startswith (prefix):
          output.append(w ord)
          break
          print ' '.join(output)

          if __name__ == "__main__":
          import sys
          extract(sys.arg v[1])

          C:\junk>sofia.p y sofia.txt
          AFFX-BioB-5_at /GEN=bioB /gb:J04423.1 /gb:J04423.1
          1415785_a_at /gb:NM_009840.1 /GEN=Cct8 /gb:BC009007.1

          Before I fix the duplicate in the first line, you need to say whether
          you really want the
          /gb:BC009007.1 in the second line thrown away -- IOW, what's the rule?
          For each prefix, either (1) get the first "word" that starts with that
          prefix or (2) get all unique such words. You choose.

          Cheers,
          John

            Comment

            • Larry Bates
              #4
              Re: extracting substrings from a file

              sofiafig@gmail. com wrote:
              Hi,
              >
              I have a file with several entries in the form:
              >
              AFFX-BioB-5_at E. coli /GEN=bioB /gb:J04423.1 NOTE=SIF
              corresponding to nucleotides 2032-2305 of /gb:J04423.1 DEF=E.coli
              7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB),
              7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and
              dethiobiotin synthetase (bioD), complete cds.
              >
              1415785_a_at /gb:NM_009840.1 /DB_XREF=gi:6753 327 /GEN=Cct8 /FEA=FLmRNA
              /CNT=482 /TID=Mm.17989.1 /TIER=FL+Stack /STK=281 /UG=Mm.17989 /LL=12469
              /DEF=Mus musculus chaperonin subunit 8 (theta) (Cct8), mRNA.
              /PROD=chaperonin subunit 8 (theta) /FL=/gb:NM_009840.1 /gb:BC009007.1
              >
              and I would like to create a file that has only the following:
              >
              AFFX-BioB-5_at /GEN=bioB /gb:J04423.1
              >
              1415785_a_at /gb:NM_009840.1 /GEN=Cct8
              >
              Could anyone please tell me how can I do it?
              >
              Many thanks in advance
              Sofia
              >
              What have your tried so far?

              Hint: split line on spaces, the first pieces is the first item you want,
              then iterate over the pieces looking for the /GEN and /gb: pieces that
              you are interested in keeping. I am assuming that /GEN= and /gb: data
              doesn't have any spaces in them. If they do, you will need to use
              regular expressions instead of split.

              -Larry Bates

                Comment

                • Paul McGuire
                  #5
                  Re: extracting substrings from a file

                  <sofiafig@gmail .comwrote in message
                  news:1157977756 .841188.8550@p7 9g2000cwp.googl egroups.com...
                  Hi,
                  >
                  I have a file with several entries in the form:
                  >
                  AFFX-BioB-5_at E. coli /GEN=bioB /gb:J04423.1 NOTE=SIF
                  corresponding to nucleotides 2032-2305 of /gb:J04423.1 DEF=E.coli
                  7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB),
                  7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and
                  dethiobiotin synthetase (bioD), complete cds.
                  >
                  1415785_a_at /gb:NM_009840.1 /DB_XREF=gi:6753 327 /GEN=Cct8 /FEA=FLmRNA
                  /CNT=482 /TID=Mm.17989.1 /TIER=FL+Stack /STK=281 /UG=Mm.17989 /LL=12469
                  /DEF=Mus musculus chaperonin subunit 8 (theta) (Cct8), mRNA.
                  /PROD=chaperonin subunit 8 (theta) /FL=/gb:NM_009840.1 /gb:BC009007.1
                  >
                  and I would like to create a file that has only the following:
                  >
                  AFFX-BioB-5_at /GEN=bioB /gb:J04423.1
                  >
                  1415785_a_at /gb:NM_009840.1 /GEN=Cct8
                  Here's a pyparsing solution that will address your immediate question, and
                  also gives you some leeway for adding other "/" options to your search.
                  Pyparsing's home page is at pyparsing.wikis paces.com.

                  -- Paul


                  data = """
                  AFFX-BioB-5_at E. coli /GEN=bioB /gb:J04423.1 NOTE=SIF
                  corresponding to nucleotides 2032-2305 of /gb:J04423.1 DEF=E.coli
                  7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB),
                  7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and
                  dethiobiotin synthetase (bioD), complete cds.

                  1415785_a_at /gb:NM_009840.1 /DB_XREF=gi:6753 327 /GEN=Cct8 /FEA=FLmRNA
                  /CNT=482 /TID=Mm.17989.1 /TIER=FL+Stack /STK=281 /UG=Mm.17989 /LL=12469
                  /DEF=Mus musculus chaperonin subunit 8 (theta) (Cct8), mRNA.
                  /PROD=chaperonin subunit 8 (theta) /FL=/gb:NM_009840.1 /gb:BC009007.1
                  """

                  from pyparsing import *

                  # create expression we are looking for:
                  # name [ junk word... ] /qualifier...
                  name = Word(alphanums, printables).set ResultsName("na me")
                  junkWord = ~(Literal("/")) + Word(printables )
                  qualifier = ("/" + Word(alphas+"_-.").setResultsN ame("key") + \
                  oneOf("= :") + \
                  Word(printables ).setResultsNam e("value"))
                  expr = name + ZeroOrMore(junk Word) + \
                  Dict(ZeroOrMore (qualifier)).se tResultsName("q uals")

                  # use parse action to repackage qualifier data to support "dict"-like
                  # access to qualifiers
                  qualifier.setPa rseAction( lambda t: (t.key,"".join( t)) )

                  # use this parse action instead if you just want whatever is
                  # after the '=' or ':' delimiter in the qualifier
                  # qualifier.setPa rseAction( lambda t: (t.key,t.value) )

                  # parse data strings, showing returned data structure
                  # (just to show what pyparsing results structure looks like)
                  for d in data.split("\n\ n"):
                  res = expr.parseStrin g(d)
                  print res.dump()
                  print
                  print

                  # now just do what the OP wanted in the first place
                  for d in data.split("\n\ n"):
                  res = expr.parseStrin g(d)
                  print res.name, res.quals["gb"], res.quals["GEN"]


                  Gives these results:
                  ['AFFX-BioB-5_at', 'E.', 'coli', [('GEN', '/GEN=bioB'), ('gb',
                  '/gb:J04423.1')]]
                  - name: AFFX-BioB-5_at
                  - quals: [('GEN', '/GEN=bioB'), ('gb', '/gb:J04423.1')]
                  - GEN: /GEN=bioB
                  - gb: /gb:J04423.1

                  ['1415785_a_at', [('gb', '/gb:NM_009840.1' ), ('DB_XREF',
                  '/DB_XREF=gi:6753 327'), ('GEN', '/GEN=Cct8'), ('FEA', '/FEA=FLmRNA'),
                  ('CNT', '/CNT=482'), ('TID', '/TID=Mm.17989.1' ), ('TIER', '/TIER=FL+Stack') ,
                  ('STK', '/STK=281'), ('UG', '/UG=Mm.17989'), ('LL', '/LL=12469'), ('DEF',
                  '/DEF=Mus')]]
                  - name: 1415785_a_at
                  - quals: [('gb', '/gb:NM_009840.1' ), ('DB_XREF', '/DB_XREF=gi:6753 327'),
                  ('GEN', '/GEN=Cct8'), ('FEA', '/FEA=FLmRNA'), ('CNT', '/CNT=482'), ('TID',
                  '/TID=Mm.17989.1' ), ('TIER', '/TIER=FL+Stack') , ('STK', '/STK=281'), ('UG',
                  '/UG=Mm.17989'), ('LL', '/LL=12469'), ('DEF', '/DEF=Mus')]
                  - CNT: /CNT=482
                  - DB_XREF: /DB_XREF=gi:6753 327
                  - DEF: /DEF=Mus
                  - FEA: /FEA=FLmRNA
                  - GEN: /GEN=Cct8
                  - LL: /LL=12469
                  - STK: /STK=281
                  - TID: /TID=Mm.17989.1
                  - TIER: /TIER=FL+Stack
                  - UG: /UG=Mm.17989
                  - gb: /gb:NM_009840.1


                  AFFX-BioB-5_at /gb:J04423.1 /GEN=bioB
                  1415785_a_at /gb:NM_009840.1 /GEN=Cct8


                    Comment

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