File header change

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February 5th, 2013, 03:42 AM

utpalmtbi

Registered User

Join Date: Feb 2013

Posts: 12

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File header change

Hello all;

I have a multi fasta file (with header[>] and sequence) in the following format:

>contig_1 # 498 # 1826 # 1 # ID=1_1;partial=00;start_type=ATG;rbs_motif=AGxAGG/AGGxGG;rbs_spacer=5-10bp;gc_cont=0.406
MNLTFDYTKEPSRDVLCIDVKSFYASVECVERG
LDPLKTMLVVMSNSENSGGLVLAASPM
>contig_2 # 1823 # 2173 # 1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.311
MKQNRKEFSSYFSRSIKQNKPLYLLLMSSETNPF
PRPVIGTFRGYVEENKIIIGEDSYSI
....
...

and i want to edit the header lines as just a simple number count:

>1
MNLTFDYTKEPSRDVLCIDVKSFYASVECVERG
LDPLKTMLVVMSNSENSGGLVLAASPM
>2
MKQNRKEFSSYFSRSIKQNKPLYLLLMSSETNPF
PRPVIGTFRGYVEENKIIIGEDSYSI
....
...

may be it's a too simple questions, but I only started to learn python and got stuck..
any idea how to do it?
thanks in advance..

February 5th, 2013, 09:47 AM

b49P23TIvg

Contributing User

Join Date: Aug 2011

Posts: 3,380

Time spent in forums: 1 Month 2 Weeks 3 Days 13 h 7 m 19 sec
Reputation Power: 383

I assume you want the number immediately following >contig_

Code:

data = '''>contig_1 # 498 # 1826 # 1 # ID=1_1;partial=00;start_type=ATG;rbs_motif=AGxAGG/AGGxGG;rbs_spacer=5-10bp;gc_cont=0.406
MNLTFDYTKEPSRDVLCIDVKSFYASVECVERG
LDPLKTMLVVMSNSENSGGLVLAASPM
>contig_2 # 1823 # 2173 # 1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.311
MKQNRKEFSSYFSRSIKQNKPLYLLLMSSETNPF
PRPVIGTFRGYVEENKIIIGEDSYSI
'''

def rewrite(LINE):
    S = '>contig_'
    return (LINE.startswith(S) and ('>' + LINE[len(S):].split()[0])) or LINE

    # traditionally this would be written as

    #if LINE.startswith(S):
    #    return '>' + LINE[len(S):].split()[0]
    #else:
    #    return LINE

for L in data.split('\n'):
    print(rewrite(L))

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February 5th, 2013, 10:28 AM