How to show only the first 20 entries

Question

The Python code here gets me the output I want. However, I need help with limiting the result to first 20 lines.

Input example is shown below,

gi|170079688|ref|YP_001729008.1| bifunctional riboflavin kinase/FMN adenylyltransferase [Escherichia coli str. K-12 substr. DH10B] MKLIRGIHNLSQAPQEGCVLTIGNFDGVHRGHRALLQGLQEEGRKRNLPVMVMLFEPQPLELFATDKAPA RLTRLREKLRYLAECGVDYVLCVRFDRRFAALTAQNFISDLLVKHLRVKFLAVGDDFRFGAGREGDFLLL QKAGMEYGFDITSTQTFCEGGVRISSTAVRQALADDNLALAESLLGHPFAISGRVVHGDELGRTIGFPTA NVPLRRQVSPVKGVYAVEVLGLGEKPLPGVANIGTRPTVAGIRQQLEVHLLDVAMDLYGRHIQVVLRKKI RNEQRFASLDELKAQIARDELTAREFFGLTKPA gi|170079689|ref|YP_001729009.1| isoleucyl-tRNA synthetase [Escherichia coli str. K-12 substr. DH10B] MSDYKSTLNLPETGFPMRGDLAKREPGMLARWTDDDLYGIIRAAKKGKKTFILHDGPPYANGSIHIGHSV NKILKDIIVKSKGLSGYDSPYVPGWDCHGLPIELKVEQEYGKPGEKFTAAEFRAKCREYAATQVDGQRKD FIRLGVLGDWSHPYLTMDFKTEANIIRALGKIIGNGHLHKGAKPVHWCVDCRSALAEAEVEYYDKTSPSI DVAFQAVDQDALKAKFAVSNVNGPISLVIWTTTPWTLPANRAISIAPDFDYALVQIDGQAVILAKDLVES VMQRIGVTDYTILGTVKGAELELLRFTHPFMGFDVPAILGDHVTLDAGTGAVHTAPGHGPDDYVIGQKYG LETANPVGPDGTYLPGTYPTLDGVNVFKANDIVVALLQEKGALLHVEKMQHSYPCCWRHKTPIIFRATPQ WFVSMDQKGLRAQSLKEIKGVQWIPDWGQARIESMVANRPDWCISRQRTWGVPMSLFVHKDTEELHPRTL ELMEEVAKRVEVDGIQAWWDLDAKEILGDEADQYVKVPDTLDVWFDSGSTHSSVVDVRPEFAGHAADMYL EGSDQHRGWFMSSLMISTAMKGKAPYRQVLTHGFTVDGQGRKMSKSIGNTVSPQDVMNKLGADILRLWVA STDYTGEMAVSDEILKRAADSYRRIRNTARFLLANLNGFDPAKDMVKPEEMVVLDRWAVGCAKAAQEDIL KAYEAYDFHEVVQRLMRFCSVEMGSFYLDIIKDRQYTAKADSVARRSCQTALYHIAEALVRWMAPILSFT ADEVWGYLPGEREKYVFTGEWYEGLFGLADSEAMNDAFWDELLKVRGEVNKVIEQARADKKVGGSLEAAV TLYAEPELSAKLTALGDELRFVLLTSGATVADYNDAPADAQQSEVLKGLKVALSKAEGEKCPRCWHYTQD VGKVAEHAEICGRCVSNVAGDGEKRKFA gi|170079690|ref|YP_001729010.1| lipoprotein signal peptidase [Escherichia coli str. K-12 substr. DH10B] MSQSICSTGLRWLWLVVVVLIIDLGSKYLILQNFALGDTVPLFPSLNLHYARNYGAAFSFLADSGGWQRW FFAGIAIGISVILAVMMYRSKATQKLNNIAYALIIGGALGNLFDRLWHGFVVDMIDFYVGDWHFATFNLA DTAICVGAALIVLEGFLPSRAKKQ

import re

id = None
header = None
seq = ''

a_file = open('e_coli.faa')

for line in a_file:
    m = re.match(">(\S+)\s+(.+)", line.rstrip())
    if m:
        if id is not None:

            print("{0} length:{1} {2}".format(id, len(seq),header))

        id, header = m.groups()
        seq = ''
    else:
        seq += line.rstrip()

Use the `slicing` operator on the `a_file`. – DirtyBit Jun 13 '20 at 19:05 — DirtyBit, Jun 13 '20 at 19:05

Red · Accepted Answer · 2020-06-13T19:27:44.357

2

In the very top, add c = 0. Then, change

        print("{0} length:{1} {2}".format(id, len(seq),header))

to

        if c < 10:
            print("{0} length:{1} {2}".format(id, len(seq),header))
            c += 1

Result with a few adjustments:

import re

id = None
header = None
seq = ''

with open('e_coli.faa') as a_file:
    for line in a_file:
        m = re.match(">(\S+)\s+(.+)", line.rstrip())
        if m:
            if id and c < 20:
                print("{0} length:{1} {2}".format(id, len(seq),header))
                c += 1

            id, header = m.groups()
            seq = ''
        else:
            seq += line.rstrip()

To read the first 20 lines of the file. you can use readlines():

Instead of:

for line in a_file:

use:

for line in a_file.readlines()[:20]:

edited Jun 13 '20 at 19:27

answered Jun 13 '20 at 19:08

Red

26,798
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This reads the first 20 lines of input file, but I need to print the first 20 lines of results instead. – lauuuuubun Jun 13 '20 at 19:16
I actually tried this approach earlier, but it's giving me an error "inconsistent use of tabs and spaces in indentation" on the print line. – lauuuuubun Jun 13 '20 at 19:24

How to show only the first 20 entries

1 Answers1